In the Purchase – Received Invoices menu, record the individual item lines (using the Add – Items button), for example, item A (5x at CZK 100/unit), item B (3x at CZK 200/unit),
also record the discount as a line item – enter "Discount" in the Name field and the discount amount in the Total Price field, for example, "-200",
a stock receipt will be generated from the received invoice (Inventory – Receipts/Issues menu),
you now need to distribute the discount – on the specific receipt, click the Services button and select the Allocate Additional Costs to Stock option,
in the wizard, fill in the Costs to Allocate field (e.g., "-200") and select the Cost Allocation Method.
The same procedure applies to issued invoices as well.